ABSTRACT
We describe a large-scale community effort to build an open-access, interoperable, and computable repository of COVID-19 molecular mechanisms - the COVID-19 Disease Map. We discuss the tools, platforms, and guidelines necessary for the distributed development of its contents by a multi-faceted community of biocurators, domain experts, bioinformaticians, and computational biologists. We highlight the role of relevant databases and text mining approaches in enrichment and validation of the curated mechanisms. We describe the contents of the Map and their relevance to the molecular pathophysiology of COVID-19 and the analytical and computational modelling approaches that can be applied for mechanistic data interpretation and predictions. We conclude by demonstrating concrete applications of our work through several use cases and highlight new testable hypotheses.
ABSTRACT
The current Coronavirus Disease 2019 (COVID-19) pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has spurred a wave of research of nearly unprecedented scale. Among the different strategies that are being used to understand the disease and develop effective treatments, the study of physical molecular interactions enables studying fine-grained resolution of the mechanisms behind the virus biology and the human organism response. Here we present a curated dataset of physical molecular interactions, manually extracted by IMEx Consortium curators focused on proteins from SARS-CoV-2, SARS-CoV-1 and other members of the Coronaviridae family. Currently, the dataset comprises over 2,200 binarized interactions extracted from 86 publications. The dataset can be accessed in the standard formats recommended by the Proteomics Standards Initiative (HUPO-PSI) at the IntAct database website (www.ebi.ac.uk/intact), and will be continuously updated as research on COVID-19 progresses.
ABSTRACT
The study of the interactome-the totality of the protein-protein interactions taking place in a cell-has experienced an enormous growth in the last few years. Biological networks representation and analysis has become an everyday tool for many biologists and bioinformatics, as these interaction graphs allow us to map and characterize signaling pathways and predict the function of unknown proteins. However, given the size and complexity of interactome datasets, extracting meaningful information from interaction networks can be a daunting task. Many different tools and approaches can be used to build, represent, and analyze biological networks. In this chapter, we will use a practical example to guide novice users through this process. We will be making use of the popular open source tool Cytoscape and of other resources such as : the PSICQUIC client to access several protein interaction repositories and the BiNGO plugin to perform GO enrichment analysis of the resulting network.